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Iron in PDB 7rtq: Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide

Protein crystallography data

The structure of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 7rtq was solved by G.I.Lepesheva, T.Y.Hargrove, Z.Wawrzak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.63 / 2.11
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.062, 75.223, 105.953, 89.49, 74.63, 63.98
R / Rfree (%) 21.1 / 23.7

Other elements in 7rtq:

The structure of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide also contains other interesting chemical elements:

Fluorine (F) 24 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide (pdb code 7rtq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 7rtq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7rtq

Go back to Iron Binding Sites List in 7rtq
Iron binding site 1 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:10.0
occ:1.00
FE A:HEM501 0.0 10.0 1.0
ND A:HEM501 1.9 9.9 1.0
NA A:HEM501 2.0 10.4 1.0
N21 A:7PW502 2.0 17.8 0.4
N21 A:7PW502 2.0 16.0 0.6
NC A:HEM501 2.1 10.9 1.0
NB A:HEM501 2.1 8.7 1.0
SG A:CYS430 2.3 13.8 1.0
C4D A:HEM501 2.9 9.0 1.0
C1D A:HEM501 2.9 10.0 1.0
C1A A:HEM501 2.9 10.7 1.0
C11 A:7PW502 3.0 19.7 0.4
C11 A:7PW502 3.0 17.9 0.6
C4A A:HEM501 3.0 11.4 1.0
C10 A:7PW502 3.1 20.1 0.4
C4C A:HEM501 3.1 10.9 1.0
C1B A:HEM501 3.1 8.8 1.0
C10 A:7PW502 3.1 18.4 0.6
C4B A:HEM501 3.1 9.2 1.0
C1C A:HEM501 3.1 10.9 1.0
CB A:CYS430 3.3 13.6 1.0
CHA A:HEM501 3.3 10.0 1.0
CHD A:HEM501 3.4 9.6 1.0
CHB A:HEM501 3.5 9.7 1.0
CHC A:HEM501 3.5 9.2 1.0
CA A:CYS430 4.0 12.8 1.0
N33 A:7PW502 4.1 20.4 0.4
N33 A:7PW502 4.1 18.4 0.6
C9 A:7PW502 4.1 20.9 0.4
C2A A:HEM501 4.1 10.4 1.0
C3D A:HEM501 4.2 10.9 1.0
C2D A:HEM501 4.2 10.9 1.0
C9 A:7PW502 4.2 18.9 0.6
C3A A:HEM501 4.2 10.9 1.0
C3C A:HEM501 4.3 12.0 1.0
C2C A:HEM501 4.3 11.0 1.0
C2B A:HEM501 4.3 9.0 1.0
C3B A:HEM501 4.4 9.4 1.0
N A:GLY432 4.7 12.8 1.0
C A:CYS430 4.8 13.7 1.0
N A:ILE431 4.9 13.2 1.0
CA A:GLY432 5.0 12.6 1.0

Iron binding site 2 out of 4 in 7rtq

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Iron binding site 2 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:9.2
occ:1.00
FE B:HEM501 0.0 9.2 1.0
ND B:HEM501 1.9 10.7 1.0
NA B:HEM501 2.0 8.9 1.0
N21 B:7PW502 2.0 15.1 0.4
N21 B:7PW502 2.0 13.1 0.6
NC B:HEM501 2.1 11.0 1.0
NB B:HEM501 2.1 9.0 1.0
SG B:CYS430 2.3 11.0 1.0
C4D B:HEM501 2.9 10.7 1.0
C1D B:HEM501 2.9 11.2 1.0
C1A B:HEM501 3.0 9.6 1.0
C11 B:7PW502 3.0 15.5 0.4
C10 B:7PW502 3.0 17.0 0.6
C4A B:HEM501 3.0 10.4 1.0
C11 B:7PW502 3.0 13.5 0.6
C10 B:7PW502 3.1 18.6 0.4
C4C B:HEM501 3.1 11.5 1.0
C1B B:HEM501 3.1 9.8 1.0
C4B B:HEM501 3.1 9.7 1.0
C1C B:HEM501 3.1 11.0 1.0
CB B:CYS430 3.3 9.7 1.0
CHA B:HEM501 3.3 10.5 1.0
CHD B:HEM501 3.4 10.7 1.0
CHB B:HEM501 3.5 9.8 1.0
CHC B:HEM501 3.5 9.9 1.0
CA B:CYS430 4.0 10.2 1.0
N33 B:7PW502 4.1 16.8 0.4
C2D B:HEM501 4.1 10.9 1.0
C3D B:HEM501 4.2 11.7 1.0
C9 B:7PW502 4.2 17.7 0.4
C9 B:7PW502 4.2 15.8 0.6
C2A B:HEM501 4.2 10.1 1.0
N33 B:7PW502 4.2 14.5 0.6
C3A B:HEM501 4.2 10.4 1.0
C3C B:HEM501 4.3 12.4 1.0
C2C B:HEM501 4.3 11.4 1.0
C2B B:HEM501 4.3 9.1 1.0
C3B B:HEM501 4.4 9.9 1.0
N B:GLY432 4.7 12.0 1.0
C B:CYS430 4.8 11.9 1.0
N B:ILE431 4.9 12.4 1.0
CA B:GLY432 5.0 13.0 1.0

Iron binding site 3 out of 4 in 7rtq

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Iron binding site 3 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:10.6
occ:1.00
FE C:HEM501 0.0 10.6 1.0
ND C:HEM501 1.9 12.6 1.0
NA C:HEM501 2.0 10.2 1.0
N21 C:7PW502 2.0 15.9 0.6
N21 C:7PW502 2.0 18.2 0.4
NC C:HEM501 2.1 12.2 1.0
NB C:HEM501 2.1 10.6 1.0
SG C:CYS430 2.3 13.1 1.0
C4D C:HEM501 2.9 12.6 1.0
C1D C:HEM501 2.9 13.0 1.0
C10 C:7PW502 2.9 20.3 0.4
C10 C:7PW502 2.9 18.3 0.6
C1A C:HEM501 3.0 11.7 1.0
C11 C:7PW502 3.0 18.8 0.6
C4A C:HEM501 3.0 10.9 1.0
C4C C:HEM501 3.0 12.4 1.0
C11 C:7PW502 3.1 20.8 0.4
C1B C:HEM501 3.1 11.1 1.0
C4B C:HEM501 3.1 10.9 1.0
C1C C:HEM501 3.1 12.8 1.0
CB C:CYS430 3.2 12.0 1.0
CHA C:HEM501 3.3 12.7 1.0
CHD C:HEM501 3.4 12.3 1.0
CHB C:HEM501 3.5 10.7 1.0
CHC C:HEM501 3.5 11.4 1.0
CA C:CYS430 3.9 11.6 1.0
C9 C:7PW502 4.1 20.7 0.4
C9 C:7PW502 4.1 18.6 0.6
N33 C:7PW502 4.1 17.8 0.6
N33 C:7PW502 4.1 20.4 0.4
C2D C:HEM501 4.2 12.5 1.0
C3D C:HEM501 4.2 13.3 1.0
C2A C:HEM501 4.2 11.6 1.0
C3A C:HEM501 4.2 11.5 1.0
C3C C:HEM501 4.3 13.4 1.0
C2C C:HEM501 4.3 13.7 1.0
C2B C:HEM501 4.3 10.8 1.0
C3B C:HEM501 4.4 11.1 1.0
N C:GLY432 4.7 14.4 1.0
C C:CYS430 4.8 13.4 1.0
N C:ILE431 4.9 13.9 1.0
CA C:GLY432 5.0 14.8 1.0

Iron binding site 4 out of 4 in 7rtq

Go back to Iron Binding Sites List in 7rtq
Iron binding site 4 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:9.8
occ:1.00
FE D:HEM501 0.0 9.8 1.0
ND D:HEM501 1.9 9.1 1.0
NA D:HEM501 2.0 8.2 1.0
N21 D:7PW502 2.1 17.8 0.4
N21 D:7PW502 2.1 15.2 0.6
NC D:HEM501 2.1 9.1 1.0
NB D:HEM501 2.1 8.2 1.0
SG D:CYS430 2.3 12.4 1.0
C4D D:HEM501 2.9 8.6 1.0
C11 D:7PW502 2.9 20.1 0.4
C1D D:HEM501 2.9 9.1 1.0
C1A D:HEM501 3.0 9.2 1.0
C11 D:7PW502 3.0 17.8 0.6
C4A D:HEM501 3.0 10.1 1.0
C4C D:HEM501 3.1 10.1 1.0
C1B D:HEM501 3.1 8.7 1.0
C4B D:HEM501 3.1 8.5 1.0
C1C D:HEM501 3.1 10.0 1.0
C10 D:7PW502 3.1 18.0 0.6
C10 D:7PW502 3.2 20.8 0.4
CB D:CYS430 3.3 11.5 1.0
CHA D:HEM501 3.3 9.2 1.0
CHD D:HEM501 3.4 8.9 1.0
CHB D:HEM501 3.5 9.5 1.0
CHC D:HEM501 3.5 8.6 1.0
CA D:CYS430 4.0 12.2 1.0
N33 D:7PW502 4.1 22.2 0.4
N33 D:7PW502 4.1 19.4 0.6
C2D D:HEM501 4.2 8.9 1.0
C3D D:HEM501 4.2 10.1 1.0
C2A D:HEM501 4.2 10.3 1.0
C3A D:HEM501 4.2 10.4 1.0
C9 D:7PW502 4.2 19.6 0.6
C9 D:7PW502 4.2 22.2 0.4
C3C D:HEM501 4.3 11.8 1.0
C2C D:HEM501 4.3 10.9 1.0
C2B D:HEM501 4.3 9.5 1.0
C3B D:HEM501 4.4 9.2 1.0
N D:GLY432 4.7 14.0 1.0
C D:CYS430 4.9 13.2 1.0
N D:ILE431 4.9 13.2 1.0
CA D:GLY432 5.0 14.2 1.0

Reference:

T.Hargrove, Z.Wawrzak, G.Rachakonda, W.Nes, F.Villalta, F.Guengerich, G.Lepesheva. Relaxed Substrate Requirements of Sterol 14ALPHA-Demethylase From Naegleria Fowleri Are Accompanied By Resistance to Inhibition J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
Page generated: Fri Aug 9 00:13:19 2024

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